Glarean's first publication on music, a modest volume entitled Isagoge in musicen, was in 1516. In it he discusses the basic elements of music; probably it was used for teaching. But his most famous book, and one of the most famous and influential works on music theory written during the Renaissance, was the Dodecachordon, which he published in Basle in 1547. This massive work includes writings on philosophy and biography in addition to music theory, and includes no less than 120 complete compositions by composers of the preceding generation (including Josquin, Ockeghem, Obrecht, Isaac and many others). In three parts, it begins with a study of Boethius, who wrote extensively on music in the sixth century; it traces the use of the musical modes in plainsong (e.g. Gregorian chant) and monophony; and it closes with an extended study of the use of modes in polyphony.[2]

The most significant feature of the Dodecachordon (literally, "12-stringed instrument") is Glarean's proposal that there are actually twelve modes, not eight, as had long been assumed, for instance in the works of the contemporary theorist Pietro Aron. The additional four modes included authentic and plagal forms of Aeolian (modes 9 and 10) and Ionian (modes 11 and 12) — the modes equivalent to minor and major scales, respectively. Glarean went so far as to say that the Ionian mode was the one most frequently used by composers in his day.[3]

The influence of his work was immense. Many later theorists, including Zarlino, accepted the twelve modes, and though the distinction between plagal and authentic forms of the modes is no longer of contemporary interest (reducing the number to six), Glarean's explanation of the musical modes remains current today.[3]